| puf3_yeast |
| ID: | 1433421932 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 253 (159.5) | ||
| Seq/Len: | 7.229 | ||
| Nf(neff/√len): | 27.0 |
HHblits Results: (2013_03)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 7.229).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 13_V | 26_G | 2.156 | 1.00 |
| 13_V | 18_V | 2.057 | 1.00 |
| 18_V | 26_G | 1.708 | 1.00 |
| 5_D | 8_E | 1.621 | 1.00 |
| 12_D | 24_E | 1.565 | 1.00 |
| 14_F | 17_Y | 1.533 | 0.99 |
| 23_F | 34_L | 1.513 | 0.99 |
| 17_Y | 21_K | 1.378 | 0.99 |
| 3_R | 33_T | 1.371 | 0.99 |
| 18_V | 22_F | 1.297 | 0.98 |
| 29_I | 33_T | 1.279 | 0.98 |
| 5_D | 28_K | 1.278 | 0.98 |
| 17_Y | 30_Q | 1.247 | 0.97 |
| 6_A | 32_N | 1.178 | 0.95 |
| 2_I | 6_A | 1.132 | 0.94 |
| 4_D | 7_I | 1.128 | 0.94 |
| 22_F | 35_V | 1.091 | 0.92 |
| 23_F | 28_K | 1.083 | 0.92 |
| 3_R | 29_I | 1.061 | 0.91 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 3gvoA | 1 | 1 | 98.6 | 0.295 | Contact Map |
| 3k49A | 3 | 1 | 98.6 | 0.308 | Contact Map |
| 3v71A | 1 | 1 | 98.5 | 0.315 | Contact Map |
| 3k62A | 1 | 1 | 98.5 | 0.317 | Contact Map |
| 4wzrA | 2 | 1 | 98.4 | 0.336 | Contact Map |
| 3bwtA | 1 | 1 | 97.8 | 0.432 | Contact Map |
| 4kf7A | 1 | 0.9143 | 10.5 | 0.824 | Contact Map |
| 2wsc4 | 1 | 0.5714 | 9.5 | 0.828 | Contact Map |
| 2dlaA | 3 | 0.8286 | 7.7 | 0.835 | Contact Map |
| 3c0kA | 2 | 0.9714 | 7.4 | 0.836 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)